cgChain: cgChain

In mskilab/gChain: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

cgChain

Description

cgChain (i.e. "CIGAR")

Processes a pairwise alignment from read to genomic coordinates inputted as a vector of CIGAR strings representing edit operations from subject to pattern. ie an insertion corresponds a gap in the subject and deletion corresponds to a gap in the pattern returns a chain that maps subject to pattern (e.g. genome space to read space)

Also, "cigar" can be a GRanges or GappedAlignment object with $cigar field where the ranges specify flanking subject coordinates of the aligned pattern (e.g. read). As by convention, subject coordinates are assumed to NOT contain flanking soft clips. Internal soft clips (if any exist - this would be unconventional use) are treated as insertions. If seqnames ("sn") input not provided then the read seqnames will be the $qname field + IsFirstMateRead part of read flag.

Returns a gChain mapping read space to genome space. cigar — ## can be character vector or GRanges GAlignment with $cigar and $qname string field)

Usage

cgChain(cigar, sn = NULL, verbose = FALSE)

Author(s)

Marcin Imielinski

mskilab/gChain documentation built on Sept. 28, 2022, 3:45 p.m.